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planemo upload for repository https://github.com/inab/trimal commit b537658ca3fbabe1bc6669efc22ac10a18f30671
author iuc
date Fri, 15 Nov 2024 08:59:10 +0000
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1 <tool id="trimal" name="trimAl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
2 <description>for automated alignment trimming</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.5</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <xrefs>
8 <xref type="bio.tools">trimal</xref>
9 </xrefs>
10 <requirements>
11 <requirement type="package" version="@TOOL_VERSION@">trimal</requirement>
12 </requirements>
13 <command detect_errors="exit_code"><![CDATA[
14 trimal -in '$in' -out '$trimmed_output' -htmlout '$html_summary' ${out_format_selector}
15 #if $trimming_mode.mode_selector == "custom"
16 -gapthreshold $trimming_mode.gapthreshold
17 -simthreshold $trimming_mode.simthreshold
18 -cons $trimming_mode.cons
19 #else:
20 $trimming_mode.mode_selector
21 #end if
22
23 ]]></command>
24 <inputs>
25 <param argument="-in" type="data" format="fasta,clustal,pir,phylip,nexus,mega" label="Alignment file (clustal, fasta, NBRF/PIR, nexus, phylip3.2, phylip)" />
26 <conditional name="trimming_mode">
27 <param name="mode_selector" type="select" label="Select trimming mode from the list">
28 <option value="-nogaps">nogaps - remove all positions with gaps in the alignment.</option>
29 <option value="-noallgaps">noallgaps - remove columns composed only by gaps.</option>
30 <option value="-gappyout">gappyout - only uses information based on gaps' distribution.</option>
31 <option value="-strict">strict - combine gappyout trimming with subsequent trimming based on an automatically selected similarity threshold. </option>
32 <option value="-strictplus">strictplus - very similar to the strict method but the final step of the algorithm is slightly different. </option>
33 <option value="-automated1">automated1 - heuristic approach to determine the optimal automatic method for trimming a given alignment. </option>
34 <option value="custom">custom mode - eliminates a specified set of columns defined by the user.</option>
35 </param>
36 <when value="-nogaps" />
37 <when value="-noallgaps"/>
38 <when value="-gappyout"/>
39 <when value="-strict"/>
40 <when value="-strictplus"/>
41 <when value="-automated1"/>
42 <when value="custom">
43 <param argument="-gapthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Gap threshold" help="1 - (fraction of sequences with a gap allowed)."/>
44 <param argument="-simthreshold" type="float" optional="true" value="0.9" min="0.0" max="1.0" label="Similarity threshold" help="Minimum average similarity allowed."/>
45 <param argument="-cons" type="integer" optional="true" value="50" min="0" max="100" label="Minimum conservance percentage" help="Minimum percentage of the positions in the original alignment to conserve."/>
46 </when>
47 </conditional>
48 <param name="out_format_selector" type="select" label="Select trimmed alignment output format from the list">
49 <option value="-clustal">CLUSTAL format</option>
50 <option value="-fasta">FASTA format</option>
51 <option value="-fasta_m10">FASTA format. Sequences name length up to 10 characters.</option>
52 <option value="-nbrf">NBRF/PIR format</option>
53 <option value="-nexus">NEXUS format</option>
54 <option value="-mega">MEGA format</option>
55 <option value="-phylip">PHYLIP/PHYLIP4 format</option>
56 <option value="-phylip_m10">PHYLIP/PHYLIP4 format. Sequences name length up to 10 characters</option>
57 <option value="-phylip_paml">PHYLIP format compatible with PAML</option>
58 <option value="-phylip_paml_m10">PHYLIP format compatible with PAML. Sequences name length up to 10 characters.</option>
59 <option value="-phylip3.2">PHYLIP3.2 format</option>
60 <option value="-phylip3.2_m10">PHYLIP3.2 format. Sequences name length up to 10 characters.</option>
61 </param>
62 </inputs>
63 <outputs>
64 <data name="trimmed_output" format="fasta" label="Trimmed alignment.">
65 <change_format>
66 <when input="out_format_selector" value="-fasta" format="fasta" />
67 <when input="out_format_selector" value="-fasta_m10" format="fasta" />
68 <when input="out_format_selector" value="-phylip" format="phylip" />
69 <when input="out_format_selector" value="-phylip_m10" format="phylip" />
70 <when input="out_format_selector" value="-phylip_paml" format="phylip" />
71 <when input="out_format_selector" value="-phylip_paml_m10" format="phylip" />
72 <when input="out_format_selector" value="-phylip3.2" format="phylip" />
73 <when input="out_format_selector" value="-phylip3.2_m10" format="phylip" />
74 <when input="out_format_selector" value="-clustal" format="clustal" />
75 <when input="out_format_selector" value="-mega" format="mega" />
76 <when input="out_format_selector" value="-nbrf" format="pir" />
77 <when input="out_format_selector" value="-nexus" format="nexus" />
78 </change_format>
79 </data>
80 <data name="html_summary" format="html" label="trimal html summary."/>
81 </outputs>
82 <tests>
83 <test expect_num_outputs="2">
84 <param name="in" value="example.009.AA.fasta"/>
85 <param name="mode_selector" value="-gappyout" />
86 <param name="out_format_selector" value="-mega" />
87 <output name="trimmed_output" file="trimmed_example.009.AA.mega" lines_diff="2"/>
88 <output name="html_summary" file="trimmed_example.009.AA.html"/>
89 </test>
90 <test expect_num_outputs="2">
91 <param name="in" value="example.009.AA.fasta"/>
92 <param name="mode_selector" value="custom" />
93 <param name="gapthreshold" value="0.5" />
94 <param name="simthreshold" value="0.5" />
95 <param name="cons" value="5" />
96 <param name="out_format_selector" value="-phylip_paml_m10" />
97 <output name="trimmed_output" file="custom_trimmed_example.009.AA.phy" ftype="phylip"/>
98 <output name="html_summary" file="custom_trimmed_example.009.AA.html"/>
99 </test>
100 </tests>
101 <help><![CDATA[
102
103 TrimAl is a tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment.
104
105 TrimAl can consider several parameters, alone or in multiple combinations, in order to select the most-reliable positions in the alignment.
106 These include the proportion of sequences with a gap, the level of residue similarity and, if several alignments for the same set of sequences are provided,
107 the consistency level of columns among alignments. Moreover, trimAl allows to manually select a set of columns and sequences to be removed from the alignment.
108
109 TrimAl implements a series of automated algorithms that trim the alignment searching for optimum thresholds based on inherent characteristics
110 of the input alignment, to be used so that the signal-to-noise ratio after alignment trimming phase is increased. Learn more about the available trimming modes here: https://trimal.readthedocs.io/en/latest/algorithms.html
111
112 Among trimAl's additional features, trimAl allows:
113
114 - getting the complementary alignment (columns that were trimmed),
115 - to compute statistics from the alignment,
116 - to select the output file format,
117 - to get a summary of trimAl's trimming in HTML and SVG formats,
118 - and many other options.
119
120 TrimAl webpage: https://trimal.readthedocs.io
121
122 License
123 -------
124 This program is free software: you can redistribute it and/or modify
125 it under the terms of the GNU General Public License as published by
126 the Free Software Foundation, the last available version.
127 ]]></help>
128 <citations>
129 <citation type="doi">doi:10.1093/bioinformatics/btp348</citation>
130 </citations>
131 </tool>